Abstract
Methods for selective covalent modification of amino acids on proteins can enable a diverse array of applications, spanning probes and modulators of protein function to proteomics1,2,3. Owing to their high nucleophilicity, cysteine and lysine residues are the most common points of attachment for protein bioconjugation chemistry through acid–base reactivity3,4. Here we report a redox-based strategy for bioconjugation of tryptophan, the rarest amino acid, using oxaziridine reagents that mimic oxidative cyclization reactions in indole-based alkaloid biosynthetic pathways to achieve highly efficient and specific tryptophan labelling. We establish the broad use of this method, termed tryptophan chemical ligation by cyclization (Trp-CLiC), for selectively appending payloads to tryptophan residues on peptides and proteins with reaction rates that rival traditional click reactions and enabling global profiling of hyper-reactive tryptophan sites across whole proteomes. Notably, these reagents reveal a systematic map of tryptophan residues that participate in cation–π interactions, including functional sites that can regulate protein-mediated phase-separation processes.
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Data availability
The experimental datasets used in this study are provided in the Supplementary Information. The MS proteomics raw data have been deposited at the MassIVE repository (https://massive.ucsd.edu/) under dataset identifier MSV000093891. Raw MS data, available at the ProteomeXchange Consortium under dataset identifiers PXD001377 and PXD005252, were used for the acetylation analysis. All AlphaFold structures with Trp-CLiC probed tryptophans were downloaded through the UniProt platform. We referred to the CPLM database (http://cplm.biocuckoo.cn) to analyse the post-translational modifications. The public database for AlphaMissense Pathogenicity Prediction was downloaded from https://console.cloud.google.com/storage/browser/dm_alphamissense;tab=objects?prefix=&forceOnObjectsSortingFiltering=false. Source data are provided with this paper.
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Acknowledgements
We acknowledge the NIH (R01 GM139245, GM79465 and ES28096 to C.J.C.; R35 GM118190 to F.D.T.; and R35 GM122451 to J.A.W.) and the Novartis-Berkeley Center for Proteomics and Chemistry Technologies for financial support. C.J.C. is a CIFAR Fellow. J.A.W. was supported by funding from the Chan Zuckerberg Biohub Investigator Program and the Harry and Dianna Hind Professorship. X.X. and D.H. are Tang Distinguished Scholars of the University of California, Berkeley. P.J.M. acknowledges the Natural Sciences and Engineering Research Council of Canada (NSERC) for a postdoctoral fellowship. S.W.M.C. was supported by the AGBT-Elaine R. Mardis Fellowship in Cancer Genomics from the Damon Runyon Cancer Research Foundation and The Genome Partnership (DRG-2395-20). A.J.B., A.G.R. and A.G.-V. were partially supported by a Chemical Biology Training Grant from the NIH (T32 GM066698) and acknowledge the National Science Foundation for graduate fellowships. A.G.-V. acknowledges the HHMI Gilliam Program for a graduate fellowship. We acknowledge NIH grant 1S10OD020062-01 for the financial support of UC Berkeley QB3 MS facilities. We thank M. B. Francis for support on MS-based protein identification, P.-Z. Mao for discussions regarding bioinformatics data analysis, and H. Celik, A. Lund and the staff at UC Berkeley’s NMR facility in the College of Chemistry (CoC-NMR) for spectroscopy assistance. Instruments in the CoC-NMR are supported in part by NIH S10OD024998. We also thank A. Killilea and her staff at UC Berkeley Cell Culture Facility for technical assistance.
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X.X., P.J.M., F.D.T. and C.J.C. designed the research and X.X. conducted the bulk of the reactivity, peptide and protein labelling, and proteomics experiments. P.J.M., S.W.M.C. and G.L. performed the molecular orbital calculations and synthesis of probe compounds. A.J.B., D.H. and A.G.R. contributed to protein and proteomic MS analyses. N.D. and A.G.-V. helped with the bioinformatics analysis. S.K.E. and J.A.W. contributed to the antibody labelling experiments. J.M.M. helped with synthetic studies. N.D. helped with the plasmid construction. X.X., F.D.T. and C.J.C. wrote the paper with input from all of the authors.
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P.J.M., X.X., F.D.T. and C.J.C. are listed as inventors on a patent application describing oxidative cyclization reagents for chemoselective tryptophan conjugation.
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Extended data figures and tables
Extended Data Fig. 1 Concept of the redox-based Trp-CLiC strategy.
a) Selectivity challenges posed by traditional probes for tryptophan labelling. Histidine, tyrosine, and cysteine can also be targeted with significantly varying degrees of labelling. b) Reaction scheme of oxidative cyclization reagents for chemoselective tryptophan bioconjugation. The Tryptophan Chemical Ligation by Cyclization (Trp-CLiC) method is highly tryptophan-selective and rapid, and it can generate stable cycloadducts with a diversity of payloads, facilitating antibody bioconjugation, unfolding stress detection, and reactive tryptophan profiling.
Extended Data Fig. 2 Screening of N-sulfonyl oxaziridine library.
a) Molecular orbital calculations on 18 disparate classes of oxaziridines revealed that the N-sulfonyl oxaziridine derivative has the lowest LUMO energy. b) Chemical structures of 18 calculated oxaziridines. The reported Hammet Substituent Constants and calculated LUMO energies are shown below the chemical structures. c) The introduction of electron-withdrawing p-nitrobenzyl or p-trifluoromethyl-benzyl groups into oxaziridine structure could decrease the LUMO energy to gain higher electrophilic reactivity. d) A N-sulfonyl oxaziridine library was designed, synthesized, and screened for tryptophan reactivity. The experimentally observed cycloadduct yields upon reaction with tryptophan are shown below the chemical structures.
Extended Data Fig. 3 Screening oxidative cyclization reagents for biocompatible tryptophan conjugation.
a) Reaction scheme for Trp-CLiC with tryptophan, where the cycloadduct is the desired product, while the hydroxyl tryptophan is the side product. b) Model of a Trp-CLiC reaction between 50 μM Ac-Trp-OMe and 60 μM oxaziridine for 10 min at room temperature in the co-solvent (PBS/MeOH =1:1). The cycloadduct and the hydroxyl tryptophan (Trp oxidized) are the proposed products. The reactions were monitored by detecting the relative quantification of peak intensity with LC-MS at 254 nm. Taking the reaction of Ac-Trp-OMe with Ox-W1 and Ox-W18 for example, the absorption peaks close to 3.1 min, 4.3 min and 6 min belong to the hydroxyl tryptophan, Ac-Trp-OMe starting material, and cycloadduct, respectively. The yield can thus be calculated by the relative peak integration of the LC-MS trace. Ox-W18 shows >91% efficacy to produce the desired cycloadduct. c) The reactivity of N-sulfonyl oxaziridine reagent Ox-W18 was also tested on other representative amino acids. d) The traceless reversibility of Cys oxidation. LC-MS trace was applied to monitor the reaction between 100 μM Fmoc-Cys-OH and 110 μM Ox-W18 for 10 min at room temperature in the co-solvent (PBS/MeOH =1:1). All Cys sites were oxidized and could be reduced upon the addition of 150 μM TCEP. e) The traceless reversibility of Met oxidation. Fmoc-Met-OH would be oxidized to form methionine sulfoxide (Met(O)). MsrA and MsrB could catalyse the reduction of S/R-Met(O), respectively. About 50% Met(O) could be reduced with high efficiency in vitro by MsrA, which catalyses the reduction of S-Met(O). We anticipate that use of both MsrA and MsrB proteins could reduce the two stereoisomers.
Extended Data Fig. 4 Testing Trp-CLiC on peptides and proteins.
a-c) Measuring spectroscopic changes and reaction kinetics between oxaziridine and tryptophan. a) The time-dependent UV-Vis absorbance of Trp-CLiC reaction between Ac-Trp-OMe (100 μM) with Ox-W18 (100 μM). As reaction proceeded, the spectroscopic changes showed the absorbance decreases at 280 nm and the intensity increases at 245 nm. b) The A260/A280 ratio, which could be easily monitored via NanoDrop spectrophotometer, could be utilized to calculate the extent of the Trp-CLiC reaction process. c) After obtaining the observed rate constants k’ under different concentrations of Ac-Trp-OMe (500 μM, 550 μM, and 600 μM), the second-order rate constant could be determined by the slope of the k’ against the Ac-Trp-OMe concentrations. d) Scheme of tryptophan modification on GLP-1. e) Crystal structure of IL8 (PDB: 2il8) featuring one native buried tryptophan residue in stick form. f) IL8 could be labelled after denaturing to expose the tryptophan residue. Results are representative of two biological replicates. g) LC-MS/MS analysis further confirmed the site-specific bioconjugation of tryptophan residue on IL8 protein. The signal peaks marked with asterisks represent the peptide products after MS cleavage and neutral loss. h) In-gel fluorescence imaging showed that oxidative cyclization reaction on BSA tryptophan residues was rapid. i) The denaturing conditions triggered an increase in the labelled tryptophan sites of Lysozyme by Trp-CLiC. Numbers of Ox-W18 targeting on representative amino acids, namely Trp, Met, Lys, Cys, Tyr, and His confirmed the specific targeting on tryptophan. Results are representative of two biological replicates. j) LC-MS/MS analysis showed that W62, the most surface-exposed site of Lysozyme, could be labelled by Trp-CLiC under native folded conditions, whereas the adjacent but more buried site W63 could only be targeted after protein denaturation. The signal peaks marked with asterisks represent the peptide products after MS cleavage and neutral loss.
Extended Data Fig. 5 Trp-CLiC enables modification of engineered antibody scaffolds and monitoring of stress-induced protein unfolding.
a-c) Screening of different buffers and pH to improve cycloadduct stability. The result showed that 50 mM Tris buffer with a pH of 7 or 8 gave the best fluorescence signal residency, while the cycloadduct is relatively stable upon treatment with 1 mM TCEP reductant. Results are representative of two biological replicates. d) Crystal structure of anti-HER2-Fab (PDB:1fve) with seven native buried tryptophan residues shown as blue stick and the surface-exposed T74 and T198 labelled in red. e) Tryptophan and methionine residue solvent accessibility of anti-HER2-Fab were analysed by the Discovery Studio program. Besides, the engineered sites (T74 or T198) were identified to be surface-exposed. f) Trp-CLiC enables single-site-specific labelling of antibodies with surface tryptophan site. g) Schematic for detection of stress-induced protein unfolding by Trp-CLiC. In the folded state, only surface, solvent-accessible tryptophan sites are accessible and less labelling will occur. In the unfolded state, internal tryptophan residues turn out to be more solvent-exposed and can react with oxaziridine oxidative cyclization reagents. h) Trp-CLiC labelling of Lysozyme under varying concentrations of guanidinium chloride (GdmCl) as a denaturant to induce unfolding showed a dose-dependent increase in tryptophan modifications with more added denaturant. Compared to the classic unfolding detection method monitoring tryptophan intrinsic fluorescence which cannot observe the unfolding intermediate status, the Trp-CLiC strategy deciphered unfolding transition mechanism which fits the three-state model. i) HeLa cells treated with vehicle control, or with the proteasome inhibitor MG-132 or the ER stress inducer tunicamycin, showed increased Trp-CLiC labelling under stress-induced unfolding conditions in whole proteomes. The error bars were shown as Mean ± s.d. of 4 independent biological repeats. Statistical analysis was performed using unpaired two-tailed Student’s t-test; P values are shown.
Extended Data Fig. 6 Investigating the proteome reactivity of N-sulfonyl oxaziridine probe.
a) Oxidative cyclization bioconjugation by Trp-CLiC was tryptophan-selective in cell lysate models. Cell lysate (1 mg/mL) was labelled with Ox-W18 (1 mM), and then clicked with azide-dye. Fluorescence imaging showed that Trp-CLiC also works for cell proteomes. Excess free Ac-Trp-OMe could significantly inhibit the Trp-CLiC labelling, indicating the chemoselectivity of our method. Results are representative of three biological replicates. b) Dose-dependent labelling of cell lysate indicated that 250 μM Ox-W18 was enough for the labelling of proteome (1 mg/mL). Results are representative of two biological replicates. c) The stability of biotin-labelled proteome was tested in 50 mM Tris buffer or PBS (pH 8), showing that Tris buffer indeed greatly enhances cycloadduct stability. Results are representative of three biological replicates. d-e) CID-cleavage mechanisms for Trp-CLiC labelling and representative spectra. d) Proposed CID-cleavage mechanisms of the acid-cleavable biotin probe cycloadduct product. The unique reporter ions 213.17 and 425.16 could be utilized to further confirm tryptophan bioconjugation by Trp-CLiC. e) Proposed CID-cleavage mechanisms of the desthiobiotin cycloadduct product. The reporter ion is m/z 484.32. The signal peaks marked with asterisks represent the peptide products after MS cleavage and neutral loss.
Extended Data Fig. 7 Bioinformatic analysis of probed tryptophan sites and proteins.
a) Venn diagram of proteins identified by DADPS biotin or desthiobiotin probes, where a total of 591 proteins were targeted by Trp-CLiC. b) Comparison of targeted proteins with the phase-separated protein database list, revealing overlapped 51 targeted proteins were reported to be phase-separated. c) Comparison of targeted proteins with the membrane-less organelle protein list, where 65.5% of targeted proteins were located in diverse membrane-less organelles. d) Drug Bank analysis of the identified 591 proteins with hyperreactive tryptophan residues, showing that 64% of them are currently classified as non-druggable. e) Gene Ontology biological pathway enrichment analysis of these 591 proteins, showing that RNA metabolism and processes pathways were significantly enriched. f) Four interaction modes of targeted tryptophans analysed by AlphaFold structure screening. g) The Trp-CLiC method revealed hyperreactive tryptophan sites, with W6 on DDX19B, W422 on FXR1, W271 on CAPZA1, and W14 on ABCF1 as representative examples. Solvent accessibilities of tryptophan residues in these three target proteins were analysed by the Discovery Studio program, indicating that the most surface-exposed tryptophan sites were probed whereas other tryptophan residues were not labelled.
Extended Data Fig. 8 Trp-CLiC targets functional cation-π interactions and reveals a privileged WxxxK cation-π motif.
a) The diversity of cation sources, such as DNA, RNA, protein, lipid, other ligands or metal ions, to form cation-π interactions with tryptophan, highlights the uniqueness of Trp cation-π interactions. b) Trp-CLiC ABPP showed the enrichment of targeting WxxxK cation-π motif. Seven examples are listed here.
Extended Data Fig. 9 Domain architectures and multiple sequence alignments of NONO proteins.
a) Crystal structure of NONO (PDB: 3sde) with one native tryptophan residue on the surface shown in stick form. b) NONO W271 located in the NOPS domain. c) NONO W271 and pairing R220 are highly conserved across diverse species, while the neighbouring R293 is not. d) The role of FBRL-W137. Mutation of W137 on the intrinsically disordered region to alanine inhibited FBRL phase separation and normal nucleolus formation. Scale bar: 5 µm. n = 3 biological independent replicates; mean ± SE. e) The role of DDX3X-W60. Mutation of W60 on the intrinsically disordered region to alanine inhibited DDX3X phase separation and stress granule formation. Scale bar: 5 µm. n = 3 biological independent replicates; mean ± SE. f) The highly surface-exposed NONO W271 could form interprotein cation-π interactions with PSPC1 R228, SFPQ R443, and R220 on another NONO protein molecule. NONO-PSPC1: PDB (3SDE); NONO-SFPQ: PDB (7LRQ). g) Model of tryptophan cation-π interactions (intraprotein or interprotein) regulating phase separation behaviour of protein targets. Image created with BioRender.com.
Extended Data Fig. 10 Lysine-tryptophan cation-π interactions could be modulated via lysine post-translational modifications.
a) Crystal structure of NPM1 C-terminal domain (PDB: 2llh) with two native tryptophan residues on the surface shown in stick form. b) NPM1 W288 and W290 are located at the C-terminus, which is the RRM domain for nucleic acid binding. c) NPM1 W288, W290, and K248 are highly conserved across diverse species, while K292 only occurs in mammals. d) Western blot after streptavidin enrichment showed that NPM1 labelling is diminished after tryptophan to alanine mutations, establishing the high specificity for Trp-CLiC method for identifying the two hyperreactive tryptophan residues of this protein target. Results are representative of two biological replicates. e) Heat map of acetylation of NPM1 lysine sites upon treatment of diverse HDAC or Sirtuin or CBP/p300 inhibitors indicated that Nicotinamide and Bufexamac could globally inhibit NPM1 de-acetylation, while A-485 could globally inhibit NPM1 acetylation. f) Scheme of proposed mechanisms of three inhibitors. g) Representative images of cells overexpressing NPM1 mutants treated with different inhibitors or stresses. Scale bar: 5 µm.
Supplementary information
Supplementary Information
General considerations and synthetic methods, NMR spectra data and Supplementary references.
Supplementary Data
Labelled sites and bioinformatic analysis.
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The uncropped gels and blots.
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Xie, X., Moon, P.J., Crossley, S.W.M. et al. Oxidative cyclization reagents reveal tryptophan cation–π interactions. Nature 627, 680–687 (2024). https://doi.org/10.1038/s41586-024-07140-6
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DOI: https://doi.org/10.1038/s41586-024-07140-6
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